I think you are a little bit confused about this.
If a person committed a crime he is not innocent no matter if this was proven or not.
Just because his innocence or non-innocence is not known, he doesn't become magically innocent. The same way a criminal does not magically change his state from innocent to non-innocent just because a judge read his verdict.
This is why people are presumed innocent - to avoid hardship for the suspect who are indeed innocent. However, since fumbling in their mouth with a cotton swap can hardly account of "hardship" taking their DNA is a reasonable measure, in particular since it helps fighting crimes.